[gmx-users] LR coulomb interaction
spoel at xray.bmc.uu.se
Wed May 4 20:25:03 CEST 2005
On Wed, 2005-05-04 at 19:37 +0200, Michal Kolinski wrote:
> I tried to evaluate LR Coulomb interaction energy for ligand and
> protein. My system contains
> membrane, ligand, TM protein and ions. I did three reruns of my
> 1) leaving charges on ligand, zeroing rest
> 2) leaving charges on protein, zeroing rest
> 3) leaving charges on protein and ligand, zeroing rest.
> Then I calculated LR Coulomb interaction energy for prot-lig (Elr_c
> Elr_c(protein-ligand) = Elr_c(ligand-ligand) + Elr_c(ligand-protein) +
principle is right, but where is the membrane and solvent? You probably
need more reruns..'
> in my case:
> 3 = 1 + Elr_c(ligand-protein) + 2
> I also included long range corrections for each of the reruns that I
> found using –rerun –debug option.
> Is this a right way to estimate LR coulomb interaction energy between
> two molecules, my estimated energy seems wrong 13.567.
> Please give me some comment on this.
> Thank you in advance.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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